Comment 1 for bug 1315729

This bug causes Gnome to automatically override custom resolutions set in xorg.conf

Quote from https://devtalk.nvidia.com/default/topic/570219/using-clone-mode-with-two-different-aspect-ratios/

 When GNOME 3 detects that a display is connected or disconnected, it will reconfigure the screen layout to match what it thinks the correct settings should be. It ignores the current configuration and the "metamodes" option in xorg.conf, and as far as I know, it also doesn't support adjusting the display borders to achieve your overscan compensation.

I believe you can disable it with this command to prevent it from changing your configuration automatically:

    dconf write /org/gnome/settings-daemon/plugins/xrandr/active false

Please note that this means you will have to manually reconfigure the screen if you want to extend the desktop to newly-connected monitors.

Aaron Plattner
NVIDIA Linux Graphics